Mutagenetix > Incidental Mutation

Incidental Mutation 'R0309:Prdm9'

25139

Institutional Source

Beutler Lab

Gene Symbol

Prdm9

Ensembl Gene

ENSMUSG00000051977

Gene Name

PR domain containing 9

Synonyms

Meisetz, repro7, Dsbc1, Rcr1, G1-419-29

MMRRC Submission

038519-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.351) question?

Stock #

R0309 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

15763341-15784616 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 15777646 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 146 (T146I)

Ref Sequence

ENSEMBL: ENSMUSP00000131871 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000147532] [ENSMUST00000167994]

AlphaFold

Q96EQ9

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128267

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130297

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139911

Predicted Effect

probably benign
Transcript: ENSMUST00000147532
AA Change: T21I

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000118454
Gene: ENSMUSG00000051977
AA Change: T21I

Domain	Start	End	E-Value	Type
Pfam:SSXRD	49	81	1.8e-19	PFAM
SET	123	243	2.56e-2	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000167994
AA Change: T146I

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: T146I

Domain	Start	End	E-Value	Type
KRAB	30	89	5.54e-8	SMART
Pfam:SSXRD	175	205	1.5e-20	PFAM
SET	248	368	2.56e-2	SMART
ZnF_C2H2	392	415	3.29e-1	SMART
ZnF_C2H2	516	535	4.74e1	SMART
ZnF_C2H2	541	563	9.73e-4	SMART
ZnF_C2H2	569	591	1.3e-4	SMART
ZnF_C2H2	597	619	1.3e-4	SMART
ZnF_C2H2	625	647	4.24e-4	SMART
ZnF_C2H2	653	675	4.24e-4	SMART
ZnF_C2H2	681	703	1.95e-3	SMART
ZnF_C2H2	709	731	5.99e-4	SMART
ZnF_C2H2	737	759	1.95e-3	SMART
ZnF_C2H2	765	787	1.95e-3	SMART
ZnF_C2H2	793	815	1.3e-4	SMART
ZnF_C2H2	821	843	1.6e-4	SMART

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 98.7%
3x: 97.6%
10x: 94.3%
20x: 86.4%

Validation Efficiency

98% (125/127)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a zinc finger protein with histone methyltransferase activity that catalyzes histone H3 lysine 4 trimethylation (H3K4me3) during meiotic prophase. This protein contains multiple domains, including a Kruppel-associated box (KRAB) domain, an SSX repression domain (SSXRD), a PRD1-BF1 and RIZ homologous region, a subclass of SET (PR/SET) domain, and a tandem array of C2H2 zinc fingers. The zinc finger array recognizes a short sequence motif, leading to local H3K4me3, and meiotic recombination hotspot activity. The observed allelic variation alters the DNA-binding sequence specificity of the protein, resulting in distinct meiotic recombination hotspots amongst individuals and populations. Multiple alternate alleles of this gene have been described. [provided by RefSeq, Jul 2015]
PHENOTYPE: Mice homozygous for a knock-out allele show decreased oocyte number, azoospermia, and sterility in both sexes due to severe impairment of the double-stranded break repair pathway, deficient pairing of homologous chromosomes, and impaired sex body formation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 126 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930402F06Rik	T	C	2: 35,266,271 (GRCm39)	D133G	possibly damaging	Het
Abcb4	A	C	5: 8,989,835 (GRCm39)	D796A	probably damaging	Het
Actg2	A	T	6: 83,496,896 (GRCm39)	V147E	probably damaging	Het
Adamts13	A	C	2: 26,877,001 (GRCm39)	T534P	probably damaging	Het
Ago1	T	C	4: 126,336,959 (GRCm39)	T249A	probably benign	Het
Ahnak	T	A	19: 8,979,859 (GRCm39)	I381N	probably damaging	Het
Akap9	A	G	5: 4,119,038 (GRCm39)	D3515G	probably benign	Het
Angptl3	T	C	4: 98,922,706 (GRCm39)	V249A	probably benign	Het
Ank	A	G	15: 27,567,658 (GRCm39)	T294A	possibly damaging	Het
Ank1	A	T	8: 23,594,825 (GRCm39)	H204L	probably damaging	Het
Apbb2	A	G	5: 66,468,331 (GRCm39)		probably benign	Het
Arhgap28	A	T	17: 68,208,424 (GRCm39)	S15T	probably benign	Het
Aspm	T	C	1: 139,410,249 (GRCm39)		probably benign	Het
Atp1a4	T	C	1: 172,062,554 (GRCm39)	E651G	probably damaging	Het
B3gnt2	A	T	11: 22,786,860 (GRCm39)	F109L	probably damaging	Het
Bpifb4	T	C	2: 153,801,603 (GRCm39)	F575L	probably damaging	Het
Calhm4	A	G	10: 33,920,043 (GRCm39)	W75R	probably damaging	Het
Calr	C	A	8: 85,569,660 (GRCm39)	K322N	probably benign	Het
Ccdc188	T	C	16: 18,037,169 (GRCm39)	S247P	possibly damaging	Het
Cdr1	T	A	X: 60,228,908 (GRCm39)	D86V	unknown	Het
Cep97	C	T	16: 55,745,421 (GRCm39)	V48I	probably damaging	Het
Chaf1b	T	A	16: 93,681,399 (GRCm39)	C6S	probably damaging	Het
Chd3	C	T	11: 69,247,844 (GRCm39)	D920N	probably damaging	Het
Clk1	T	C	1: 58,452,192 (GRCm39)		probably benign	Het
Cntnap3	T	A	13: 64,905,250 (GRCm39)		probably benign	Het
Col12a1	T	A	9: 79,507,293 (GRCm39)		probably null	Het
Col17a1	G	T	19: 47,659,801 (GRCm39)		probably benign	Het
Coq7	T	A	7: 118,128,940 (GRCm39)	I32F	possibly damaging	Het
Cox6a2	A	T	7: 127,805,107 (GRCm39)	F59I	probably damaging	Het
Cpq	A	G	15: 33,594,297 (GRCm39)	D436G	probably damaging	Het
Ctso	G	A	3: 81,852,168 (GRCm39)		probably null	Het
Cxadr	A	T	16: 78,131,836 (GRCm39)	H274L	probably benign	Het
Cyp2c40	A	T	19: 39,766,495 (GRCm39)	C367S	possibly damaging	Het
Cyp2c70	T	G	19: 40,149,115 (GRCm39)	M344L	possibly damaging	Het
Defa35	G	A	8: 21,555,871 (GRCm39)	V77I	probably benign	Het
Dhx57	A	G	17: 80,582,310 (GRCm39)	Y432H	probably damaging	Het
Dhx9	A	T	1: 153,341,441 (GRCm39)	D601E	probably benign	Het
Dnah7a	C	G	1: 53,444,849 (GRCm39)	D3952H	probably damaging	Het
Dnah9	C	A	11: 65,917,798 (GRCm39)		probably benign	Het
Dstyk	C	A	1: 132,384,602 (GRCm39)		probably benign	Het
Efcab2	T	A	1: 178,303,469 (GRCm39)		probably benign	Het
Ehbp1l1	T	C	19: 5,770,598 (GRCm39)	E287G	possibly damaging	Het
Epgn	A	G	5: 91,180,073 (GRCm39)	T87A	probably benign	Het
Erc2	A	C	14: 27,863,182 (GRCm39)	E803A	probably damaging	Het
Fer	A	G	17: 64,446,011 (GRCm39)	*454W	probably null	Het
Glyr1	T	C	16: 4,849,836 (GRCm39)	D179G	probably damaging	Het
Gm12830	T	A	4: 114,702,173 (GRCm39)		probably benign	Het
Gm9922	C	A	14: 101,967,129 (GRCm39)		probably benign	Het
Gsta3	C	T	1: 21,335,118 (GRCm39)	P200S	possibly damaging	Het
Hmgxb3	G	A	18: 61,288,200 (GRCm39)		probably benign	Het
Hsh2d	G	A	8: 72,954,304 (GRCm39)	D229N	probably benign	Het
Il16	T	C	7: 83,371,762 (GRCm39)	K15E	probably damaging	Het
Kcnip2	T	A	19: 45,782,514 (GRCm39)		probably benign	Het
Kdm4c	T	C	4: 74,263,804 (GRCm39)	V696A	probably benign	Het
Kdr	A	G	5: 76,107,587 (GRCm39)		probably benign	Het
Klhl33	T	G	14: 51,128,868 (GRCm39)	H787P	probably damaging	Het
Klk14	A	T	7: 43,343,769 (GRCm39)	T159S	probably benign	Het
Lancl2	A	G	6: 57,680,117 (GRCm39)	N16D	probably damaging	Het
Lemd3	T	C	10: 120,773,015 (GRCm39)	N583S	possibly damaging	Het
Map3k4	TGCTGGCTTCAGGGCCACAGTCCGCTG	TGCTG	17: 12,489,902 (GRCm39)		probably null	Het
Mpl	T	G	4: 118,303,235 (GRCm39)		probably benign	Het
Myh7b	T	C	2: 155,472,592 (GRCm39)		probably benign	Het
Mylk	A	C	16: 34,732,667 (GRCm39)		probably benign	Het
Myof	A	T	19: 37,969,714 (GRCm39)	M316K	probably benign	Het
Nfib	T	A	4: 82,214,974 (GRCm39)	N543I	probably damaging	Het
Nfix	A	G	8: 85,448,403 (GRCm39)	S375P	probably damaging	Het
Nkrf	T	C	X: 36,153,769 (GRCm39)	Q171R	probably damaging	Het
Nmnat2	T	A	1: 152,952,747 (GRCm39)		probably benign	Het
Npffr2	G	A	5: 89,731,206 (GRCm39)	E379K	probably benign	Het
Npr2	T	C	4: 43,640,904 (GRCm39)		probably benign	Het
Nup98	A	C	7: 101,801,635 (GRCm39)	D212E	probably null	Het
Nwd2	T	C	5: 63,964,561 (GRCm39)	Y1382H	probably damaging	Het
Ocstamp	T	C	2: 165,237,912 (GRCm39)	R451G	possibly damaging	Het
Or52s1	T	A	7: 102,861,928 (GRCm39)	I287K	probably damaging	Het
Or6c6c	A	G	10: 129,541,008 (GRCm39)	D87G	probably benign	Het
Pabpc1	C	T	15: 36,597,737 (GRCm39)	A551T	possibly damaging	Het
Pard3	A	T	8: 128,103,378 (GRCm39)		probably benign	Het
Pcdhb12	G	T	18: 37,569,174 (GRCm39)	V107L	probably benign	Het
Pik3cd	A	T	4: 149,747,677 (GRCm39)	V22D	probably damaging	Het
Pkd1l2	A	G	8: 117,724,315 (GRCm39)	V2396A	probably damaging	Het
Pnpla7	T	C	2: 24,877,207 (GRCm39)	I167T	probably damaging	Het
Pphln1	A	T	15: 93,339,588 (GRCm39)	H114L	possibly damaging	Het
Ppm1h	A	G	10: 122,756,687 (GRCm39)	N444S	probably damaging	Het
Prrc2a	A	G	17: 35,369,891 (GRCm39)		probably benign	Het
Prrx1	T	C	1: 163,140,128 (GRCm39)	D26G	possibly damaging	Het
Ptpn5	T	C	7: 46,729,042 (GRCm39)	E495G	probably damaging	Het
Rab23	A	C	1: 33,773,942 (GRCm39)		probably null	Het
Ralgps1	C	T	2: 33,047,935 (GRCm39)	M348I	probably benign	Het
Ranbp2	A	G	10: 58,315,690 (GRCm39)	T2137A	probably benign	Het
Rapgef4	G	T	2: 72,056,374 (GRCm39)	G654V	probably benign	Het
Rc3h2	A	T	2: 37,269,020 (GRCm39)		probably benign	Het
Reg2	G	A	6: 78,383,169 (GRCm39)	A39T	possibly damaging	Het
Sema4d	C	A	13: 51,879,347 (GRCm39)	V7F	probably benign	Het
Sgip1	T	C	4: 102,772,354 (GRCm39)		probably benign	Het
Sgpl1	C	T	10: 60,949,216 (GRCm39)		probably null	Het
Shisa9	G	A	16: 11,814,987 (GRCm39)	V212M	probably damaging	Het
Shq1	G	A	6: 100,550,588 (GRCm39)	P450L	probably benign	Het
Sin3a	A	G	9: 57,018,196 (GRCm39)	T872A	probably benign	Het
Sipa1l3	C	T	7: 29,047,775 (GRCm39)	R1371Q	probably benign	Het
Skint8	T	C	4: 111,796,064 (GRCm39)	V246A	probably benign	Het
Slc22a20	A	T	19: 6,022,985 (GRCm39)	V386D	probably damaging	Het
Slc28a2b	A	T	2: 122,348,034 (GRCm39)	T253S	probably benign	Het
Slc2a7	G	A	4: 150,242,528 (GRCm39)		probably benign	Het
Slc35a2	T	A	X: 7,755,901 (GRCm39)	Y48N	probably damaging	Het
Slc4a2	G	T	5: 24,639,344 (GRCm39)	S413I	probably damaging	Het
Sntg2	T	C	12: 30,276,772 (GRCm39)	T427A	probably benign	Het
Soat1	T	C	1: 156,270,023 (GRCm39)	Y132C	probably damaging	Het
Stn1	G	T	19: 47,490,112 (GRCm39)	H342N	probably benign	Het
Tarbp1	T	A	8: 127,165,667 (GRCm39)		probably benign	Het
Tas2r113	A	C	6: 132,870,341 (GRCm39)	K123T	probably damaging	Het
Tbck	C	T	3: 132,440,168 (GRCm39)	Q504*	probably null	Het
Tenm3	C	T	8: 48,794,069 (GRCm39)	C380Y	probably damaging	Het
Tent4a	A	T	13: 69,648,051 (GRCm39)	V781E	possibly damaging	Het
Triobp	A	G	15: 78,860,740 (GRCm39)	D1389G	probably damaging	Het
Trpm4	A	T	7: 44,958,130 (GRCm39)	F780I	probably damaging	Het
Tubb4a	G	T	17: 57,388,182 (GRCm39)	Y281*	probably null	Het
Txndc15	T	C	13: 55,872,395 (GRCm39)	F261S	probably damaging	Het
Ube3b	T	C	5: 114,557,530 (GRCm39)		probably benign	Het
Unc5c	G	C	3: 141,439,694 (GRCm39)	V196L	probably benign	Het
Upf3a	G	A	8: 13,845,500 (GRCm39)		probably null	Het
Vmn2r20	T	C	6: 123,363,063 (GRCm39)	K574E	probably benign	Het
Vps50	A	G	6: 3,536,853 (GRCm39)	M275V	possibly damaging	Het
Xrcc5	A	G	1: 72,346,735 (GRCm39)		probably benign	Het
Zbtb18	T	C	1: 177,276,182 (GRCm39)	L505S	probably damaging	Het
Zbtb41	T	C	1: 139,366,722 (GRCm39)	I567T	probably damaging	Het
Zfp598	T	C	17: 24,897,558 (GRCm39)		probably benign	Het

Other mutations in Prdm9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01302:Prdm9	APN	17	15,773,608 (GRCm39)	missense	probably benign	0.11
IGL02322:Prdm9	APN	17	15,783,110 (GRCm39)	missense	probably damaging	0.99
IGL02354:Prdm9	APN	17	15,783,109 (GRCm39)	missense	probably damaging	1.00
IGL02361:Prdm9	APN	17	15,783,109 (GRCm39)	missense	probably damaging	1.00
IGL02724:Prdm9	APN	17	15,783,522 (GRCm39)	missense	probably benign	0.07
IGL03120:Prdm9	APN	17	15,765,193 (GRCm39)	missense	probably benign
berlin	UTSW	17	15,782,702 (GRCm39)	missense	probably damaging	0.96
R0173:Prdm9	UTSW	17	15,764,297 (GRCm39)	missense	probably benign	0.00
R0173:Prdm9	UTSW	17	15,764,275 (GRCm39)	missense	probably benign	0.02
R1420:Prdm9	UTSW	17	15,764,638 (GRCm39)	missense	probably damaging	1.00
R3498:Prdm9	UTSW	17	15,783,207 (GRCm39)	splice site	probably benign
R3714:Prdm9	UTSW	17	15,777,623 (GRCm39)	nonsense	probably null
R4118:Prdm9	UTSW	17	15,764,275 (GRCm39)	missense	probably benign	0.02
R4369:Prdm9	UTSW	17	15,764,708 (GRCm39)	missense	probably benign	0.14
R4691:Prdm9	UTSW	17	15,773,640 (GRCm39)	missense	probably benign	0.03
R4742:Prdm9	UTSW	17	15,773,783 (GRCm39)	missense	probably damaging	0.99
R4910:Prdm9	UTSW	17	15,764,585 (GRCm39)	missense	probably benign	0.08
R5056:Prdm9	UTSW	17	15,782,679 (GRCm39)	missense	possibly damaging	0.93
R5130:Prdm9	UTSW	17	15,764,729 (GRCm39)	missense	probably benign	0.00
R5175:Prdm9	UTSW	17	15,777,713 (GRCm39)	missense	probably benign	0.04
R5187:Prdm9	UTSW	17	15,783,155 (GRCm39)	missense	probably damaging	0.98
R5213:Prdm9	UTSW	17	15,775,416 (GRCm39)	missense	probably damaging	0.98
R5270:Prdm9	UTSW	17	15,773,625 (GRCm39)	missense	probably benign	0.16
R5635:Prdm9	UTSW	17	15,782,702 (GRCm39)	missense	probably damaging	0.96
R6753:Prdm9	UTSW	17	15,765,218 (GRCm39)	missense	probably benign	0.00
R6857:Prdm9	UTSW	17	15,764,518 (GRCm39)	missense	probably benign	0.04
R7041:Prdm9	UTSW	17	15,765,257 (GRCm39)	missense	possibly damaging	0.56
R7355:Prdm9	UTSW	17	15,765,497 (GRCm39)	missense	probably benign	0.01
R7410:Prdm9	UTSW	17	15,765,259 (GRCm39)	missense	possibly damaging	0.73
R7570:Prdm9	UTSW	17	15,775,914 (GRCm39)	missense	probably benign	0.14
R7571:Prdm9	UTSW	17	15,783,526 (GRCm39)	missense	probably damaging	0.98
R7575:Prdm9	UTSW	17	15,764,890 (GRCm39)	missense	probably damaging	1.00
R7593:Prdm9	UTSW	17	15,764,867 (GRCm39)	missense	possibly damaging	0.81
R7664:Prdm9	UTSW	17	15,775,833 (GRCm39)	missense	probably damaging	0.99
R7755:Prdm9	UTSW	17	15,765,226 (GRCm39)	missense	probably damaging	1.00
R7817:Prdm9	UTSW	17	15,779,311 (GRCm39)	missense	probably damaging	1.00
R7875:Prdm9	UTSW	17	15,773,804 (GRCm39)	nonsense	probably null
R8110:Prdm9	UTSW	17	15,774,960 (GRCm39)	missense	probably damaging	1.00
R8222:Prdm9	UTSW	17	15,765,035 (GRCm39)	missense	possibly damaging	0.93
R8405:Prdm9	UTSW	17	15,764,456 (GRCm39)	missense	probably benign	0.22
R8695:Prdm9	UTSW	17	15,765,019 (GRCm39)	missense	probably damaging	1.00
R8947:Prdm9	UTSW	17	15,764,270 (GRCm39)	missense	possibly damaging	0.96
X0021:Prdm9	UTSW	17	15,773,734 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- AGATTGCCCAAGTCCCAGTACCTC -3'
(R):5'- CCTCAAGCCTGAAAGAAGCCTGAAG -3'

Sequencing Primer
(F):5'- AGTCCCAGTACCTCCATGTGAG -3'
(R):5'- GAAAGCCTAGCAGATGGCCTC -3'

Posted On

2013-04-16